Hprc banner tamu.png

Difference between revisions of "Terra:QuickStart"

From TAMU HPRC
Jump to: navigation, search
(Navigating Terra & Storage Quotas)
(tamubatch)
 
(59 intermediate revisions by 10 users not shown)
Line 4: Line 4:
 
'''Access to Terra is granted with the condition that you will understand and adhere to all TAMU HPRC and Terra-specific policies.'''  
 
'''Access to Terra is granted with the condition that you will understand and adhere to all TAMU HPRC and Terra-specific policies.'''  
  
General policies can be found on the [[HPRC:Policies | HPRC Policies page]].
+
General policies can be found on the [https://hprc.tamu.edu/policies/ HPRC Policies page].
  
Terra-specific policies, which are similar to Ada, can be found on the [[Terra:Policies | Terra Policies page]].  
+
Terra-specific policies, which are similar to Grace, can be found on the [[Terra:Policies | Terra Policies page]].
  
 
== Accessing Terra ==
 
== Accessing Terra ==
  
Most access to Terra is done via a secure shell session.
+
<!--'''For convenience, this topic has been summarized in a short video lesson, which you can view [https://www.youtube.com/watch?v=dypaj5uHpqQ here]. Otherwise, feel free to continue reading.'''-->
 +
 
 +
<!--Most access to Terra is done via a secure shell session.
  
 
Users on '''Windows''' computers use either [http://www.putty.org/ PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm]. If MobaXterm works on your computer, it is usually easier to use.
 
Users on '''Windows''' computers use either [http://www.putty.org/ PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm]. If MobaXterm works on your computer, it is usually easier to use.
Line 16: Line 18:
 
Users on '''Mac''' and '''Linux/Unix''' should use whatever SSH-capable terminal is available on their system.
 
Users on '''Mac''' and '''Linux/Unix''' should use whatever SSH-capable terminal is available on their system.
  
The command to connect to Terra is as follows. Be sure to replace [NetID] with your TAMU NetID.
+
The command to connect to Terra is as follows. Be sure to replace [NetID] with your TAMU NetID.  
  ssh [NetID]@terra.tamu.edu
+
  [user1@localhost ~]$ '''ssh ''NetID''@terra.tamu.edu'''
 +
<font color=teal>'''Note:''' In this example ''[user1@localhost ~]$'' represents the command prompt on your local machine.</font> <br>
 +
Your login password is the same that used on [https://howdy.tamu.edu/ Howdy]. You will not see your password as your type it into the login prompt.-->
 +
 
 +
Most access to Terra is done via a secure shell session. In addition, '''two-factor authentication''' is required to login to any cluster.
 +
 
 +
Users on '''Windows''' computers use either [http://www.putty.org/ PuTTY] or [http://mobaxterm.mobatek.net/ MobaXterm]. If MobaXterm works on your computer, it is usually easier to use. When starting an ssh session in PuTTY, choose the connection type 'SSH', select port 22, and then type the hostname 'terra.tamu.edu'. For MobaXterm, select 'Session', 'SSH', and then remote host 'terra.tamu.edu'. Check the box to specify username and type your NetID. After selecting 'Ok', you will be prompted for Duo Two Factor Authentication. For more detailed instructions, visit the [https://hprc.tamu.edu/wiki/Two_Factor#MobaXterm Two Factor Authentication] page.
 +
 
 +
Users on '''Mac''' and '''Linux/Unix''' should use whatever SSH-capable terminal is available on their system. The command to connect to Terra is as follows. Be sure to replace [NetID] with your TAMU NetID.
 +
[user1@localhost ~]$ '''ssh ''[NetID]''@terra.tamu.edu'''
 +
<font color=teal>'''Note:''' In this example ''[user1@localhost ~]$'' represents the command prompt on your local machine.</font> <br>
 
Your login password is the same that used on [https://howdy.tamu.edu/ Howdy]. You will not see your password as your type it into the login prompt.
 
Your login password is the same that used on [https://howdy.tamu.edu/ Howdy]. You will not see your password as your type it into the login prompt.
 +
 +
=== Off Campus Access ===
 +
Please visit [https://hprc.tamu.edu/wiki/HPRC:Remote_Access this page] to find information on accessing Terra remotely.
 +
 +
For more detailed instructions on how to access our systems, please see the [[HPRC:Access | HPRC Access page]].
 +
  
 
== Navigating Terra & Storage Quotas ==
 
== Navigating Terra & Storage Quotas ==
Line 25: Line 43:
  
 
You can navigate to your ''home'' directory with the following command:
 
You can navigate to your ''home'' directory with the following command:
  cd /home/[NetID]
+
  [NetID@terra1 ~]$ '''cd /home/''NetID'''''
  
 
Your ''scratch'' directory has more storage space than your ''home'' directory and is recommended for general purpose use. You can navigate to your ''scratch'' directory with the following command:
 
Your ''scratch'' directory has more storage space than your ''home'' directory and is recommended for general purpose use. You can navigate to your ''scratch'' directory with the following command:
  cd /scratch/user/[NetID]
+
  [NetID@terra1 ~]$ '''cd /scratch/user/''NetID'''''
  
 
You can navigate to ''scratch'' or ''home'' easily by using their respective environment variables.  
 
You can navigate to ''scratch'' or ''home'' easily by using their respective environment variables.  
  
 
Navigate to ''scratch'' with the following command:
 
Navigate to ''scratch'' with the following command:
  cd $SCRATCH
+
  [NetID@terra1 ~]$ '''cd $SCRATCH'''
  
 
Navigate to ''home'' with the following command:
 
Navigate to ''home'' with the following command:
  cd $HOME
+
  [NetID@terra1 ~]$ '''cd $HOME'''
  
 
<font color=purple>
 
<font color=purple>
Your ''scratch'' directory is restricted to 1TB/50,000 files of storage. This storage quota is '''expandable''' upon request.
+
Your ''scratch'' directory is restricted to 1TB/250,000 files of storage. This storage quota is '''expandable''' upon request. A user's ''scratch directory'' is '''NOT''' backed up.
 
   
 
   
Your ''home'' directory is restricted to 10GB/10,000 files of storage. This storage quota is '''not expandable'''.
+
Your ''home'' directory is restricted to 10GB/10,000 files of storage. This storage quota is '''not expandable'''.  A user's ''home'' directory is backed up on a nightly basis.
 
</font>
 
</font>
  
 
You can see the current status of your storage quotas with:
 
You can see the current status of your storage quotas with:
  showquota
+
  [NetID@terra1 ~]$ '''showquota'''
 +
 
 +
If you need a storage quota increase, please contact us with justification and the expected length of time that you will need the quota increase.
 +
 
 +
== Transferring Files ==
 +
 
 +
Files can be transferred to Terra using the ''scp'' command or a file transfer program.
 +
 
 +
Our users most commonly utilize:
 +
* [https://winscp.net/eng/download.php WinSCP] - Straightforward, legacy
 +
* [https://filezilla-project.org/ FileZilla Client] - Easy to use, additional features, available on most platforms
 +
* [https://mobaxterm.mobatek.net/features.html MobaXterm Graphical SFTP] - Included with MobaXterm
 +
 
 +
See our [Terra-Filezilla example video] for a demonstration of this process.
 +
 
 +
<font color=teal>'''Advice:''' while GUIs are acceptable for file transfers, the cp and scp commands are much quicker and may significantly benefit your workflow.</font>
 +
 
 +
=== Reliably Transferring Large Files ===
 +
 
 +
For files larger than several GB, you will want to consider the use of a more fault-tolerant utility such as rsync.
 +
[NetID@terra1 ~]$ '''rsync -av [-z] ''localdir/ userid@remotesystem:/path/to/remotedir/'''''
 +
 
 +
<!-- See our [Terra-rsync example video] for a demonstration of this process. -->
 +
<!-- [Insert info on glob, ftn] -->
 +
 
 +
== Managing Project Accounts ==
 +
The batch system will charge SUs from the either the account specified in the job parameters, or from your default account (if this parameter is omitted). To avoid errors in SU billing, you can view your active accounts, and set your default account using the [https://hprc.tamu.edu/wiki/HPRC:myproject myproject] command.
 +
 
 +
== Finding Software ==
 +
 
 +
Software on Terra is loaded using '''modules'''.
 +
 
 +
A list of the most popular software on our systems is available on the [[:SW | HPRC Available Software]] page.
 +
 
 +
To '''find''' ''most'' available software on Terra, use the following command:
 +
[NetID@terra1 ~]$ '''module avail'''
 +
 
 +
To '''search for''' particular software by keyword, use:
 +
[NetID@terra1 ~]$ '''module spider ''keyword'''''
 +
 
 +
To load a module, use:
 +
[NetID@terra1 ~]$ '''module load ''moduleName'''''
 +
 
 +
To list all currently loaded modules, use:
 +
[NetID@terra1 ~]$ '''module list'''
 +
 
 +
To remove all currently loaded modules, use:
 +
[NetID@terra1 ~]$ '''module purge'''
 +
 
 +
If you need '''new software''' or '''an update''', please contact us with your request.
 +
 
 +
There are restrictions on what software we can install. There is also regularly a queue of requested software installations.
 +
 
 +
<font color=teal>Please account for '''delays''' in your installation request timeline. </font>
 +
 
  
If you need a storage quota increase, please contact us with justification and the expected length of time that you will need the extended quota.
+
== Running Your Program / Preparing a Job File ==
  
==The Batch System==
+
In order to properly run a program on Terra, you will need to create a job file and submit a job to the batch system. The batch system is a load distribution implementation that ensures convenient and fair use of a shared resource. Submitting jobs to a batch system allows a user to reserve specific resources with minimal interference to other users. All users are required to submit resource-intensive processing to the compute nodes through the batch system - <font color=red> attempting to circumvent the batch system is not allowed.</font>
The batch system is a load distribution implementation that ensures convenient and fair use of a shared resource. Submitting jobs to a batch system allows a user to reserve specific resources with minimal interference to other users. All users are required to submit resource-intensive processing to the compute nodes through the batch system - <font color=red> attempting to circumvent the batch system is not allowed.</font>
 
  
 
On Terra, '''Slurm''' is the batch system that provides job management.  
 
On Terra, '''Slurm''' is the batch system that provides job management.  
 
More information on '''Slurm''' can be found in the [[Terra:Batch | Terra Batch]] page.
 
More information on '''Slurm''' can be found in the [[Terra:Batch | Terra Batch]] page.
  
== Running Your Program / Preparing a Job File ==
 
 
In order to properly run a program on Terra, you will need to create a job file and submit a job.
 
  
The simple example job file below requests 1 core on 1 node with 2.5GB of RAM for 1 hour. Note that typical nodes on Terra have 28 cores with 120GB of usable memory and ensure that your job requirements will fit within these restrictions. Any modules that need to be loaded or executable commands will replace the "#First Executable Line" in this example.
+
The simple example job file below requests 1 core on 1 node with 2.5GB of RAM for 1.5 hours. Note that typical nodes on Terra have 28 cores with 120GB of usable memory and ensure that your job requirements will fit within these restrictions. Any modules that need to be loaded or executable commands will replace the ''"#First Executable Line"'' in this example.
 
  #!/bin/bash
 
  #!/bin/bash
 
  ##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
 
  ##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
Line 66: Line 134:
 
    
 
    
 
  ##NECESSARY JOB SPECIFICATIONS
 
  ##NECESSARY JOB SPECIFICATIONS
  #SBATCH -J JobExample1       #Set the job name to "JobExample1"
+
  #SBATCH --job-name=JobExample1     #Set the job name to "JobExample1"
  #SBATCH -t 01:30:00         #Set the wall clock limit to 1hr and 30min
+
  #SBATCH --time=01:30:00           #Set the wall clock limit to 1hr and 30min
  #SBATCH -N 1                #Request 1 node
+
  #SBATCH --ntasks=1                #Request 1 task
  #SBATCH --ntasks-per-node=1   #Request 1 task/core per node
+
  #SBATCH --ntasks-per-node=1       #Request 1 task/core per node
  #SBATCH --mem=2560M         #Request 2560MB (2.5GB) per node
+
  #SBATCH --mem=2560M               #Request 2560MB (2.5GB) per node
  #SBATCH -o Example1Out.%j    #Send stdout/err to "Example1Out.[jobID]"
+
  #SBATCH --output=Example1Out.%j    #Send stdout/err to "Example1Out.[jobID]"
 
   
 
   
 
  #First Executable Line
 
  #First Executable Line
Line 77: Line 145:
 
Note: If your job file has been written on an older Mac or DOS workstation, you will need to use "dos2unix" to remove certain characters that interfere with parsing the script.
 
Note: If your job file has been written on an older Mac or DOS workstation, you will need to use "dos2unix" to remove certain characters that interfere with parsing the script.
  
  dos2unix MyJob.slurm
+
  [NetID@terra1 ~]$ '''dos2unix ''MyJob.slurm'''''
  
 
More information on '''job options''' can be found in the [[Terra:Batch#Building_Job_Files | Building Job Files]] section of the [[Terra:Batch | Terra Batch]] page.
 
More information on '''job options''' can be found in the [[Terra:Batch#Building_Job_Files | Building Job Files]] section of the [[Terra:Batch | Terra Batch]] page.
Line 85: Line 153:
 
== Submitting and Monitoring Jobs ==
 
== Submitting and Monitoring Jobs ==
 
Once you have your job file ready, it is time to submit your job. You can submit your job to slurm with the following command:
 
Once you have your job file ready, it is time to submit your job. You can submit your job to slurm with the following command:
  [user1@terra1 ~]$ sbatch MyJob.slurm  
+
  [NetID@terra1 ~]$ '''sbatch ''MyJob.slurm'''''
 
  Submitted batch job 3606
 
  Submitted batch job 3606
  
 
After the job has been submitted, you are able to monitor it with several methods.  
 
After the job has been submitted, you are able to monitor it with several methods.  
To see all of your jobs, use the following command:
+
To see the status of all of your jobs, use the following command:
  [user1@terra1 ~]$ squeue -u user1
+
  [NetID@terra1 ~]$ '''squeue -u ''NetID'''''
 
  JOBID      NAME                USER                    PARTITION  NODES CPUS STATE      TIME        TIME_LEFT  START_TIME          REASON      NODELIST             
 
  JOBID      NAME                USER                    PARTITION  NODES CPUS STATE      TIME        TIME_LEFT  START_TIME          REASON      NODELIST             
  3606        myjob2              user1                   short      1    3    RUNNING    0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]   
+
  3606        myjob2              NetID                   short      1    3    RUNNING    0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]   
  
To cancel a job while it is pending or running, use the following command:
+
To see the status of one job, use the following command, where ''XXXX'' is the JobID:
  [user1@terra1 ~]$ scancel 3606
+
  [NetID@terra1 ~]$ '''squeue --job ''XXXX'''''
 
+
JOBID      NAME                USER                    PARTITION  NODES CPUS STATE      TIME        TIME_LEFT  START_TIME          REASON      NODELIST           
{| class="wikitable" style="text-align: center;"
+
XXXX        myjob2              NetID                  short      1    3    RUNNING    0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]
|+ Job Monitoring and Control Commands
 
!Function
 
!Command
 
!Example
 
|-
 
|Submit a job
 
|sbatch [script_file]
 
|sbatch FileName.job
 
|-
 
|Cancel/Kill a job
 
|scancel [job_id]
 
|scancel 101204
 
|-
 
|Check status of a single job
 
|squeue --job [job_id]
 
|squeue --job 101204
 
|-
 
|Check status of all <br> jobs for a user
 
|squeue -u [user_name]
 
|squeue -u terraUser1
 
|}
 
 
 
More information on '''submitting''' and '''monitoring''' Slurm jobs can be found in the [[:Terra:Batch#Job_Submission | Job Submission]] section of the [[:Terra:Batch | Terra Batch System]] page.
 
 
 
== Additional Topics ==
 
 
 
=== Translating Ada/LSF <--> Terra/Slurm ===
 
 
 
The [[:HPRC:Batch_Translation | HPRC Batch Translation]] page contains information on '''converting''' between LSF, PBS, and Slurm.
 
 
 
Our staff has also written some example jobs for specific software. These software-specific examples can be seen on the [[:SW | Individual Software Pages]] where available.
 
 
 
=== Finding Software ===
 
 
 
Software on Terra is loaded using '''modules'''.
 
 
 
You can see the most popular software on the [[:SW | HPRC Available Software]] page.
 
  
You can find ''most'' available software on Terra with the following command:
+
To cancel a job, use the following command, where ''XXXX'' is the JobID:
  module avail
+
  [NetID@terra1 ~]$ '''scancel ''XXXX'''''
  
You can search for particular software by keyword using:
+
More information on [[:Terra:Batch#Job_Submission | Job Submission]] and [[:Terra:Batch#Job_Monitoring_and_Control_Commands | Job Monitoring]] Slurm jobs can be found at the [[:Terra:Batch | Terra Batch System]] page.
module spider ''keyword''
 
  
If you need '''new software''' or '''an update''', please contact us with your request.
+
== tamubatch ==
  
There are restrictions on what software we can install. There is also regularly a queue of requested software installations.  
+
'''tamubatch''' is an automatic batch job script that submits jobs for the user without the need of writing a batch script on the Grace and Terra clusters. The user just needs to provide the executable commands in a text file and tamubatch will automatically submit the job to the cluster. There are flags that the user may specify which allows control over the parameters for the job submitted.
  
<font color=teal>Account for '''delays''' in your installation request timeline. </font>
+
''tamubatch is still in beta and has not been fully developed. Although there are still bugs and testing issues that are currently being worked on, tamubatch can already submit jobs to both the Grace and Terra clusters if given a file of executable commands. ''
  
=== Transferring Files ===
+
For more information, visit [https://hprc.tamu.edu/wiki/SW:tamubatch this page.]
  
Files can be transferred to Terra using the ''scp'' command or a file transfer program.
+
== Graphic User Interfaces (Visualization) ==
 
 
Our users most commonly utilize:
 
* [[https://winscp.net/eng/download.php WinSCP]] - Straightforward, legacy
 
* [[https://filezilla-project.org/ FileZilla Client]] - Easy to use, additional features, available on most platforms
 
* [[https://mobaxterm.mobatek.net/features.html MobaXterm Graphical SFTP]] - Included with MobaXterm
 
 
 
See our [Terra-Filezilla example video] for a demonstration of this process.
 
 
 
<font color=teal>'''Advice:''' while GUIs are acceptable for file transfers, the cp and scp commands are much quick and may significantly benefit your workflow.</font>
 
 
 
[Insert info on glob, rsync, ftn]
 
 
 
=== Graphic User Interfaces (Visualization) ===
 
  
 
The use of GUIs on Terra is a more complicated process than running non-interactive jobs or doing resource-light interactive processing.
 
The use of GUIs on Terra is a more complicated process than running non-interactive jobs or doing resource-light interactive processing.
Line 169: Line 186:
 
You have '''two options''' for using GUIs on Terra.
 
You have '''two options''' for using GUIs on Terra.
  
The '''first option''' is to run on the login node. When doing this, you '''must''' observe the fair-use policy of login node usage. Users commonly violate these policies by accident, resulting in terminated processes, confusion, and warnings from our admins.
+
The '''first option''' is to use the [https://portal.hprc.tamu.edu/ Open On Demand Portal], which is a web interface to our clusters. Users must be connected to the campus network either directly or via VPN to access the portal. More information can be found [https://hprc.tamu.edu/wiki/SW:Portal here], or on our [https://www.youtube.com/watch?v=dqa2ZzsEmQs&list=PLHR4HLly3i4aJJDxKTZIpxyJG6uSqgAgd YouTube channel]
 
 
The '''second option''' is to use a VNC job. This method is outside the scope of this guide. See the [[Terra:Remote-Viz | Terra Remote Visualization]] page for more information.
 
  
[[Category: Terra]]
+
The '''second option''' is to run on the login node. When doing this, you '''must''' observe the fair-use policy of login node usage. Users commonly violate these policies by accident, resulting in terminated processes, confusion, and warnings from our admins.

Latest revision as of 15:39, 15 November 2021

Terra Quick Start Guide

Terra Usage Policies

Access to Terra is granted with the condition that you will understand and adhere to all TAMU HPRC and Terra-specific policies.

General policies can be found on the HPRC Policies page.

Terra-specific policies, which are similar to Grace, can be found on the Terra Policies page.

Accessing Terra

Most access to Terra is done via a secure shell session. In addition, two-factor authentication is required to login to any cluster.

Users on Windows computers use either PuTTY or MobaXterm. If MobaXterm works on your computer, it is usually easier to use. When starting an ssh session in PuTTY, choose the connection type 'SSH', select port 22, and then type the hostname 'terra.tamu.edu'. For MobaXterm, select 'Session', 'SSH', and then remote host 'terra.tamu.edu'. Check the box to specify username and type your NetID. After selecting 'Ok', you will be prompted for Duo Two Factor Authentication. For more detailed instructions, visit the Two Factor Authentication page.

Users on Mac and Linux/Unix should use whatever SSH-capable terminal is available on their system. The command to connect to Terra is as follows. Be sure to replace [NetID] with your TAMU NetID.

[user1@localhost ~]$ ssh [NetID]@terra.tamu.edu

Note: In this example [user1@localhost ~]$ represents the command prompt on your local machine.
Your login password is the same that used on Howdy. You will not see your password as your type it into the login prompt.

Off Campus Access

Please visit this page to find information on accessing Terra remotely.

For more detailed instructions on how to access our systems, please see the HPRC Access page.


Navigating Terra & Storage Quotas

When you first access Terra, you will be within your home directory. This directory has smaller storage quotas and should not be used for general purpose.

You can navigate to your home directory with the following command:

[NetID@terra1 ~]$ cd /home/NetID

Your scratch directory has more storage space than your home directory and is recommended for general purpose use. You can navigate to your scratch directory with the following command:

[NetID@terra1 ~]$ cd /scratch/user/NetID

You can navigate to scratch or home easily by using their respective environment variables.

Navigate to scratch with the following command:

[NetID@terra1 ~]$ cd $SCRATCH

Navigate to home with the following command:

[NetID@terra1 ~]$ cd $HOME

Your scratch directory is restricted to 1TB/250,000 files of storage. This storage quota is expandable upon request. A user's scratch directory is NOT backed up.

Your home directory is restricted to 10GB/10,000 files of storage. This storage quota is not expandable. A user's home directory is backed up on a nightly basis.

You can see the current status of your storage quotas with:

[NetID@terra1 ~]$ showquota

If you need a storage quota increase, please contact us with justification and the expected length of time that you will need the quota increase.

Transferring Files

Files can be transferred to Terra using the scp command or a file transfer program.

Our users most commonly utilize:

See our [Terra-Filezilla example video] for a demonstration of this process.

Advice: while GUIs are acceptable for file transfers, the cp and scp commands are much quicker and may significantly benefit your workflow.

Reliably Transferring Large Files

For files larger than several GB, you will want to consider the use of a more fault-tolerant utility such as rsync.

[NetID@terra1 ~]$ rsync -av [-z] localdir/ userid@remotesystem:/path/to/remotedir/


Managing Project Accounts

The batch system will charge SUs from the either the account specified in the job parameters, or from your default account (if this parameter is omitted). To avoid errors in SU billing, you can view your active accounts, and set your default account using the myproject command.

Finding Software

Software on Terra is loaded using modules.

A list of the most popular software on our systems is available on the HPRC Available Software page.

To find most available software on Terra, use the following command:

[NetID@terra1 ~]$ module avail

To search for particular software by keyword, use:

[NetID@terra1 ~]$ module spider keyword

To load a module, use:

[NetID@terra1 ~]$ module load moduleName

To list all currently loaded modules, use:

[NetID@terra1 ~]$ module list

To remove all currently loaded modules, use:

[NetID@terra1 ~]$ module purge

If you need new software or an update, please contact us with your request.

There are restrictions on what software we can install. There is also regularly a queue of requested software installations.

Please account for delays in your installation request timeline.


Running Your Program / Preparing a Job File

In order to properly run a program on Terra, you will need to create a job file and submit a job to the batch system. The batch system is a load distribution implementation that ensures convenient and fair use of a shared resource. Submitting jobs to a batch system allows a user to reserve specific resources with minimal interference to other users. All users are required to submit resource-intensive processing to the compute nodes through the batch system - attempting to circumvent the batch system is not allowed.

On Terra, Slurm is the batch system that provides job management. More information on Slurm can be found in the Terra Batch page.


The simple example job file below requests 1 core on 1 node with 2.5GB of RAM for 1.5 hours. Note that typical nodes on Terra have 28 cores with 120GB of usable memory and ensure that your job requirements will fit within these restrictions. Any modules that need to be loaded or executable commands will replace the "#First Executable Line" in this example.

#!/bin/bash
##ENVIRONMENT SETTINGS; CHANGE WITH CAUTION
#SBATCH --export=NONE        #Do not propagate environment
#SBATCH --get-user-env=L     #Replicate login environment
  
##NECESSARY JOB SPECIFICATIONS
#SBATCH --job-name=JobExample1     #Set the job name to "JobExample1"
#SBATCH --time=01:30:00            #Set the wall clock limit to 1hr and 30min
#SBATCH --ntasks=1                 #Request 1 task
#SBATCH --ntasks-per-node=1        #Request 1 task/core per node
#SBATCH --mem=2560M                #Request 2560MB (2.5GB) per node
#SBATCH --output=Example1Out.%j    #Send stdout/err to "Example1Out.[jobID]"

#First Executable Line

Note: If your job file has been written on an older Mac or DOS workstation, you will need to use "dos2unix" to remove certain characters that interfere with parsing the script.

[NetID@terra1 ~]$ dos2unix MyJob.slurm

More information on job options can be found in the Building Job Files section of the Terra Batch page.

More information on dos2unix can be found on the dos2unix section of the HPRC Available Software page.

Submitting and Monitoring Jobs

Once you have your job file ready, it is time to submit your job. You can submit your job to slurm with the following command:

[NetID@terra1 ~]$ sbatch MyJob.slurm
Submitted batch job 3606

After the job has been submitted, you are able to monitor it with several methods. To see the status of all of your jobs, use the following command:

[NetID@terra1 ~]$ squeue -u NetID
JOBID       NAME                USER                    PARTITION   NODES CPUS STATE       TIME        TIME_LEFT   START_TIME           REASON      NODELIST            
3606        myjob2              NetID                   short       1     3    RUNNING     0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]  

To see the status of one job, use the following command, where XXXX is the JobID:

[NetID@terra1 ~]$ squeue --job XXXX
JOBID       NAME                USER                    PARTITION   NODES CPUS STATE       TIME        TIME_LEFT   START_TIME           REASON      NODELIST            
XXXX        myjob2              NetID                   short       1     3    RUNNING     0:30        00:10:30    2016-11-27T23:44:12  None        tnxt-[0340]  

To cancel a job, use the following command, where XXXX is the JobID:

[NetID@terra1 ~]$ scancel XXXX

More information on Job Submission and Job Monitoring Slurm jobs can be found at the Terra Batch System page.

tamubatch

tamubatch is an automatic batch job script that submits jobs for the user without the need of writing a batch script on the Grace and Terra clusters. The user just needs to provide the executable commands in a text file and tamubatch will automatically submit the job to the cluster. There are flags that the user may specify which allows control over the parameters for the job submitted.

tamubatch is still in beta and has not been fully developed. Although there are still bugs and testing issues that are currently being worked on, tamubatch can already submit jobs to both the Grace and Terra clusters if given a file of executable commands.

For more information, visit this page.

Graphic User Interfaces (Visualization)

The use of GUIs on Terra is a more complicated process than running non-interactive jobs or doing resource-light interactive processing.

You have two options for using GUIs on Terra.

The first option is to use the Open On Demand Portal, which is a web interface to our clusters. Users must be connected to the campus network either directly or via VPN to access the portal. More information can be found here, or on our YouTube channel

The second option is to run on the login node. When doing this, you must observe the fair-use policy of login node usage. Users commonly violate these policies by accident, resulting in terminated processes, confusion, and warnings from our admins.